7ZG6

TacA1 antitoxin

PDB DOI: https://doi.org/10.2210/pdb7ZG6/pdb

Classification: ANTITOXIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-01 Released: 2023-10-11
Deposition Author(s): Grabe, G.J., Morgan, R.M.L., Helaine, S.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular stripping underpins derepression of a toxin-antitoxin system.

Grabe, G.J., Giorgio, R.T., Wieczor, M., Gollan, B., Sargen, M., Orozco, M., Hare, S.A., Helaine, S.

(2024) Nat Struct Mol Biol

PubMed: 38538913 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01253-2
Primary Citation of Related Structures:
7ZG5, 7ZG6

PubMed Abstract:
Transcription factors control gene expression; among these, transcriptional repressors must liberate the promoter for derepression to occur. Toxin-antitoxin (TA) modules are bacterial elements that autoregulate their transcription by binding the promoter in a T:A ratio-dependent manner, known as conditional cooperativity. The molecular basis of how excess toxin triggers derepression has remained elusive, largely because monitoring the rearrangement of promoter-repressor complexes, which underpin derepression, is challenging. Here, we dissect the autoregulation of the Salmonella enterica tacAT3 module. Using a combination of assays targeting DNA binding and promoter activity, as well as structural characterization, we determine the essential TA and DNA elements required to control transcription, and we reconstitute a repression-to-derepression path. We demonstrate that excess toxin triggers molecular stripping of the repressor complex off the DNA through multiple allosteric changes causing DNA distortion and ultimately leading to derepression. Thus, our work provides important insight into the mechanisms underlying conditional cooperativity.

Organizational Affiliation

Department of Microbiology, Harvard Medical School, Boston, MA, USA. grzegorz_grabe@hms.harvard.edu.

Macromolecule Content

Total Structure Weight: 20.88 kDa
Atom Count: 880
Modelled Residue Count: 104
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1778 domain-containing protein	A, B	91	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: A3104_05255, A3S30_03565, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3X15_00845, A3X55_00325... A3104_05255, A3S30_03565, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3X15_00845, A3X55_00325, A3Y76_07970, A4N07_08005, A4O05_01325, A4O41_02030, A4R48_08935, A6D61_12035, AAA76_07485, AAB27_15580, AAB79_05115, AAC35_03625, ADQ28_10175, AF497_21965, AGM99_05600, AHN93_12130, AIT36_00965, AKH62_19105, AL144_05695, AL168_00235, AL184_01805, AQ530_13115, AU613_00250, AVA38_12925, AVC05_10875, AVL16_07530, AWT30_08430, AXX99_15530, B1265_05360, B1398_03145, B1642_07215, B1P38_10085, B2E31_12120, B4V59_11835, B4W90_05735, B6362_03215, B7Q27_05355, B8Y16_03500, B8Z46_06180, B9C90_03095, B9C96_10075, B9M14_05165, B9O84_11710, BBQ66_14315, BG493_00970, BIC00_08660, BIC13_03220, BK110_05555, BKM50_23075, BMS46_12650, BMU56_14435, BZ203_17650, BZZ88_00325, C5W43_16875, CA117_15910, CAC56_00970, CAC59_00965, CB102_05780, CB119_09125, CB198_11360, CB380_04130, CB535_00770, CB570_01825, CB646_00870, CBM67_04325, CBM76_05660, CBZ90_17945, CC339_13495, CC403_04170, CC453_00825, CC652_10795, CC971_08240, CCP17_05605, CDZ72_00830, CE70_05375, CED07_09525, CEQ70_11810, CFF58_15570, CFF59_19345, CHN22_12865, CIX60_11710, CPS79_04635, CQO33_02710, CSG22_15805, CVR97_16715, D4361_00880, D4387_02960, D4422_08010, D5823_11460, D5N86_07595, D5N95_00880, D5O82_10090, D5P17_09705, D5X47_03750, D5Y28_11875, D6422_07755, D6J79_03215, D8S24_00875, DLB93_00880, DLR28_04665, DMI89_02725, DMO92_11765, DN165_06005, DNB97_10970, DNM27_08060, DNZ37_00880, DO533_01630, DP680_00880, DPB42_14145, DPD91_14800, DPF41_20265, DPF68_06590, DPS76_07075, DQD22_06090, DQR44_03755, DRM14_09660, DRT38_10160, DRT61_12455, DRV05_07095, DSF94_03190, DSG41_05900, DTF68_09765, DU071_11260, DU223_00815, DU657_08780, DU879_06935, DUV75_05405, DWU22_19580, DY580_11365, DYM27_07925, E0935_00855, E1A11_05885, E6W45_05500, EBD14_00860, EBK21_06270, EC404_08070, EEQ30_12970, EER35_04045, EHB09_10535, EL822_04920, ELS01_06375, EPB30_06160, EQG93_08445, EVY71_04545, EW905_00790, F0D96_17675, F2P00_07215, F3Q97_08560, F3R12_09955, F9G02_14055, F9O44_13860, FE758_17770, FEM52_12105, FGZ46_08045, FJM64_04970, FQC24_05140, G0038_06515, G0040_06835, G0042_12205, G0045_10420, G0047_05575, G0048_09090, G0051_05645, G0052_10845, G0059_05920, G0061_08170, G0062_08755, G0063_08645, G0067_09250, G0069_08825, G0070_07845, G0071_07185, G0072_20045, G0074_10225, G0076_07480, G0077_09020, G0080_10875, G0084_11635, G0086_11145, G0087_09090, G0088_08175, G0089_05200, G0090_03750, G0094_03980, G0100_14430, G0101_08275, G0102_07975, G0111_07605, G0113_09075, G0117_05810, G0123_09090, G0124_08815, G0148_07850, G0157_08505, G0170_09825, G0A05_14075, G0A28_05465, G0A32_06825, G0A39_18140, G0A43_17520, G0A44_05550, G0A46_06310, G0A50_04840, G0A51_06360, G0A52_16360, G0A53_03430, G0A56_14045, G0A58_04545, G0A60_05590, G0A61_07875, G0A63_17195, G0A66_04925, G0A67_08445, G0A68_18030, G0A70_04840, G0A73_06565, G0A76_16870, G0A79_08455, G0A92_06600, G0A96_06095, G0A97_04965, G0B03_06365, G0B05_02820, G0B07_02725, G0B08_03810, G0B12_00880, G0B28_10240, G0B96_06335, G0C03_03190, G0C04_07190, G0C34_08565, G0E15_12925, G0E20_13295, G0G84_14085, G0J24_05055, G0J26_08460, G0J27_00095, G0J28_06230, G0J31_03640, G0J33_04725, G0J34_09505, G0J36_06530, G0J37_09245, G0J40_08070, G0J43_05190, G0J44_09360, G0J45_06495, G0J46_07005, G0J47_09125, G0J49_07265, G0J50_09965, G0J51_08105, G0J53_03235, G0J55_05945, G0J58_04230, G0J59_20595, G0J62_02515, G0J65_11725, G0J66_02900, G0J67_06095, G0J69_03030, G0J71_03030, G0J73_12265, G0J76_03040, G0J79_08505, G0J81_05720, G0J82_07345, G0J85_05720, G0J89_12195, G0J92_11440, G0J94_12605, G0J96_11010, G0J97_05440, G0K00_10905, G0K02_08285, G0K03_06860, G0K04_04250, G0K05_00240, G0K07_03030, G0K10_07455, G0K13_06135, G0K15_04670, G0K16_11380, G0K18_09305, G0K19_03650, G0K20_01175, G0K23_06850, G0K25_00860, G0K26_09485, G0K28_12265, G0K30_06250, G0K31_02845, G0K32_21510, G0K33_05630, G0K37_00860, G0K38_10400, G0K39_00335, G0K41_00085, G0K42_08445, G0K44_09515, G0K46_05720, G0K47_10440, G0K48_11600, G0K49_12390, G0K52_13585, G0K53_13740, G0K56_12050, G0K58_17230, G0K59_13125, G0K61_08780, G0K65_07070, G0K68_05005, G0K70_08325, G0K72_03975, G0K74_16835, G0K75_06960, G0K78_11500, G0K80_19145, G0K83_05585, G0K84_13785, G0K85_10750, G0K88_003091, G0K89_000478, G0K90_000620, G0K94_000430, G0K95_000292, G0L00_000826, G0L02_000147, G0L03_04555, G0L06_01490, G0L07_01390, G0L10_04810, G0L14_03745, G0L15_14085, G0L18_01845, G0L19_04630, G0L20_03085, G0L24_03300, G0L25_01965, G0L29_02895, G0L31_11005, G0L32_05770, G0L34_00205, G0L35_02995, G0L36_06695, G0L37_03740, G0L38_01885, G0L40_13160, G0L42_04645, G0L48_07890, G0L49_00765, G0L51_03265, G0L52_00205, G0L55_04440, G0L59_01970, G0L62_04765, G0L63_03260, G0L65_18350, G0L67_02995, G0L68_05120, G0L70_10470, G0L73_04820, G0L76_03925, G0L77_17435, G0L78_01720, G0L79_04450, G0L83_11890, G0L85_15975, G0L86_000812, G0L88_02390, G0L89_04205, G0L91_04730, G0L93_17950, G0L96_03385, G0L98_18590, G0M00_19130, G0M05_16255, G0M06_000797, G0M13_000386, G0M14_02960, G0M16_02050, G0M18_000979, G0M21_11905, G0M22_000387, G0M25_000386, G0M26_03060, G0M29_000386, G0M30_05720, G0M33_12160, G0M35_05655, G0M36_14210, G0M38_01790, G0M39_00205, G0M40_05845, G0M41_07030, G0M45_06700, G0M46_000387, G0M48_000386, G0M51_18885, G0M53_03230, G0M55_04405, G0M56_01960, G0M58_01960, G0M63_03225, G0M65_01595, G0M67_04405, G0N45_04990, G0N48_08870, G0N51_12275, G0N53_04100, G0N55_07635, G0N57_04235, G0N58_04670, G0N59_10615, G0N60_09690, G0N61_05575, G0N62_05150, G0N64_07260, G0N65_06200, G0N66_09410, G0N67_07280, G0N71_08275, G0N75_10630, G0N78_06745, G0N82_06845, G0N84_07815, G0N85_04100, G0N86_11270, G0N88_07695, G0N89_06295, G0N90_07775, G0N92_16350, G0N94_02910, G0N95_11325, G0N98_10685, G0N99_03385, G0O00_03935, G0O03_07580, G0O10_06805, G0O14_02520, G0O15_13895, G0O18_14755, G0O19_09410, G0O20_06675, G0O22_05735, G0O25_08960, G0O27_07635, G0O31_08180, G0O32_05755, G0O36_06595, G0O37_08385, G0O39_05570, G0O40_13490, G0O41_08050, G0O42_08170, G0O43_09115, G0O44_05530, G0O47_08630, G0O52_07975, G0O55_07350, G0O57_07915, G0O58_10050, G0O59_14250, G0O60_09400, G0O63_04985, G0O66_13570, G0O68_07395, G0O70_08825, G0O71_08830, G0O74_07800, G0O75_07515, G0O77_08670, G0O78_08440, G0O80_07565, G0O81_03470, G0O82_10280, G0O84_08825, G0O85_05775, G0O86_10380, G0O87_07970, G0O88_03850, G0O89_06015, G0O92_08935, G0O93_04240, G0O94_13365, G0O97_02240, G0O99_13400, G0P00_15000, G0P01_02695, G0P02_06645, G0P05_12915, G0P06_08355, G0P08_09050, G0P12_13305, G0P13_05680, G0P17_06760, G0P18_07640, G0P19_05475, G0P24_03400, G0P26_08830, G0P28_08900, G0P30_08560, G0P31_10875, G0P36_12775, G0P37_02110, G0P41_15205, G0P44_03655, G0P45_07105, G0P48_07965, G0P49_00335, G0P52_05645, G0P53_00330, G0P56_10010, G0P57_08830, G0P58_04990, G0P63_06775, G0P65_04880, G0P67_10125, G0P68_07255, G0P69_00325, G0P73_13720, G0P75_01825, G0P76_03245, G1N61_05970, G1N64_05885, G1N66_05875, G1N68_05880, G1N71_05895, G1N72_05885, G1N86_05895, G1N87_05895, G1N91_06610, G1O00_03055, G1O02_05890, G1O04_05895, G1O05_05885, G1O08_05875, G1O10_07975, G1O12_05895, G1O16_05890, G1O17_05965, G1O18_05890, G1O20_05895, G1O23_05895, G1O25_05875, G1O26_05895, G1O27_05955, G1O28_05970, G1O29_05955, G1O32_05875, G1O34_05965, G1O38_06300, G1O40_05895, G1O43_05880, G1O46_03050, G1O48_05970, G1O49_05965, G1O51_05890, G1O53_05950, G1O62_05890, G1O63_05880, G1O65_05970, G1O67_07430, G1O68_05895, G1O69_05895, G1O71_09050, G1O72_05970, G1O76_05970, G1O77_05895, G1O80_05965, G1O81_05890, G1O83_05960, G1O84_05970, G1O87_05970, G1O88_05970, G1O89_05895, G1O90_05970, G1O93_05960, G1O94_05955, G1O96_05965, G1P02_05955, G1P03_05995, G1P06_05950, G1P09_03685, G1P10_05895, G1P12_05970, G1P14_00860, G1P15_08090, G1P17_05970, G1P19_05965, G1P23_05965, G1P24_05885, G1P25_05970, G1P26_05890, G1P29_05975, G1P31_05950, G1P35_05895, G1P36_05890, G1P37_05920, G1P40_03125, G1P44_05890, G1P45_05960, G1P47_05965, G1P48_05970, G1P51_05970, G1P52_05920, G1P53_05920, G1P54_05970, G1P55_05965, G1P56_05950, G1P57_05970, G1P58_05955, G1P59_05970, G1P61_08375, G1P64_05970, G1P67_05965, G1P69_05875, G1P72_10265, G1P75_05895, G1P76_05880, G1P78_03700, G1P83_03715, G1P84_05890, G1P87_05960, G1P90_05715, G1P91_05955, G1Q03_05890, G1Q08_05185, G1Q67_05960, G1Q78_05595, G1Q81_05965, G1Q83_05970, G1Q84_05625, G1Q85_05925, G1Q86_05880, G1Q88_03055, G1Q90_05955, G1Q91_05895, G1Q93_04950, G1Q96_05860, G1Q98_05895, G1Q99_05955, G1R01_05875, G1R02_03055, G1R03_05965, G1R04_05970, G1R08_05945, G1R13_05450, G1R15_05045, G1R20_03845, G1R21_05650, G1R22_03130, G1R23_03685, G1R27_05870, G1R28_05970, G1R29_05965, G1R30_05970, G1R31_06165, G1R36_05970, G1R38_05890, G1R40_03130, G1R42_03055, G1R44_05965, G1R45_07650, G1R47_03700, G1R48_03395, G1R51_05880, G1R52_08035, G1R53_05950, G1R63_05970, G1R69_00860, G1R87_03685, G1R93_05880, G1S02_05970, G2203_08010, G2212_16670, G2218_10055, G2221_14440, G2279_12050, G2290_12650, G2793_13330, G2918_13520, G2951_06210, G3221_002687, G3230_003613, G3231_002106, G3247_003536, G3248_001297, G3254_000041, G3263_002896, G3270_003435, G3275_000730, G3312_001759, G3336_003551, G3357_001662, G3369_000598, G3433_000039, G3460_000171, G3464_002693, G3593_003627, G3A35_06005, G3V06_000996, G3V14_003115, G3V17_000446, G3V21_001922, G3V56_000559, G3V57_001798, G3X03_001804, G4189_001061, G4190_000739, G4192_000812, G4198_000464, G4201_002101, G4202_001475, G4A01_003277, G4A73_001924, G4A83_004288, G4A85_000794, G4A87_001128, G4B68_002273, G4B72_002691, G4B74_000681, G4C74_000731, G4D32_002863, G4D46_002458, G4F88_00970, G4F89_00970, G4F91_00970, G4F92_00970, G4G47_002693, G4G62_000410, G4G67_002618, G4G68_003383, G4G75_001677, G4G76_001466, G4G79_002670, G4G97_002413, G4H00_000793, G4H04_004572, G4H07_003669, G4H08_000532, G4H18_000731, G4H21_000731, G4H24_000730, G4H63_001252, G4I66_003375, G4J07_001211, G4J08_002078, G4J11_000370, G4J12_000193, G4J18_002023, G4J20_003006, G4J37_004094, G4J39_002351, G4J41_001527, G4J45_002735, G4J90_001712, G4K02_000287, G4K03_000466, G4O54_000644, G4O56_001570, G4O59_000812, G4O60_000681, G4O67_000089, G4O69_001284, G4P29_001084, G4P83_001851, G4P85_000793, G4P89_003493, G4P91_001061, G4P93_001762, G4Q12_003651, G4Q28_000730, G4Q31_000728, G4Q50_002142, G4Q52_001801, G4Q59_002806, G4Q60_000793, G4Q63_002240, G4Q67_002883, G4Q94_003297, G4R01_000792, G4R02_002284, G4R15_002694, G4R16_000737, G4W68_003700, G4W73_000555, G4W86_000984, G4W87_000730, G4W88_000730, G4W91_000171, G4Y10_003993, G9269_000834, G9302_000793, G9304_001305, G9305_003574, G9309_000405, G9313_000793, G9314_004791, G9367_001474, G9381_000651, G9C24_000382, G9C41_000996, G9C46_000850, G9C47_000681, G9C49_001054, G9C57_000728, G9C64_002283, G9G03_000497, G9G04_003111, G9G34_001926, G9G36_000577, G9G45_002412, G9G50_002044, G9G62_002044, G9W19_001373, G9W28_001671, G9W45_000065, G9W52_002689, G9W63_002268, G9W65_000728, G9W79_002140, G9W95_000731, G9W96_002672, G9X40_002429, GB021_12045, GB040_11900, GB055_08450, GB076_09505, GB106_05935, GB114_08425, GB120_05560, GB122_13965, GB131_01480, GB139_06875, GB171_04135, GB209_06840, GB221_07870, GB224_00855, GB238_15785, GB280_05645, GB321_07520, GB331_07235, GB339_13210, GB342_05095, GB368_12215, GB372_06145, GB416_14990, GB452_06040, GB459_14220, GB466_12015, GB505_11895, GB510_10150, GB551_04205, GB567_10895, GB645_16180, GBS44_03925, GBS58_06025, GBV53_06495, GBV54_10940, GBV60_02935, GBW03_15445, GBW44_14930, GBW52_04530, GBW76_13765, GBX12_15340, GBX20_14950, GBX46_08290, GBX55_07645, GBX64_03960, GBY13_11225, GBY23_15345, GBY73_06075, GBZ51_19885, GBZ55_00575, GCZ80_15175, GEZ01_02980, GJE27_05655, GJE28_04530, GNA88_002718, GNA97_002865, GNA99_002432, GNB28_002419, GNB36_000624, GNB86_001092, GNC11_000727, GNC19_001070, GNC45_001165, GNC75_002133, GNC95_001305, GT380_05455, GTH60_03850, GTH62_02950, GTH63_08330, GTH66_08435, GTH67_11860, GTH68_08760, GTH70_03975, GTH72_08690, GTH73_05575, GTH75_06305, GTH77_02135, GTH78_08775, GTH79_06410, GTH81_13490, GTH85_09070, GTH87_09400, GTH89_05040, GTH90_06140, GTH91_00195, GTH93_08825, GTH94_05825, GTH99_03645, GXC51_05525, GXC56_05525, GXG40_05525, GYI58_17275, GYI62_000736, GYI77_09250, GYJ04_02110, GYJ24_05825, GYJ27_19115, GYJ28_003979, GYJ30_10035, GYJ32_11340, GYJ53_05965, GYJ59_05485, GYJ60_05955, H8S97_18675, JJB80_18360, JJB81_18355, KP44_05620, NG06_06920, R035_07945, Z700_03565, ZV17_16945, ZV33_03590, ZX03_04645, ZY40_05085
UniProt
Find proteins for A0A2J0RDY6 (Salmonella typhimurium) Explore A0A2J0RDY6 Go to UniProtKB: A0A2J0RDY6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2J0RDY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.99	α = 90
b = 68.99	β = 90
c = 69.47	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Grabe, G.J.

Morgan, R.M.L.

Helaine, S.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/M009629/1
European Research Council (ERC)	European Union	757369
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/D524840/1
Wellcome Trust	United Kingdom	202926/Z/16/Z